Added the details on import with Phonopy an ASE in the user guide

UserGuide/gettingstarted.rst

@@ -531,6 +531,69 @@ The structure is read from the first dynamical matrix (usually the gamma point).
 An experimental interface to phonopy is under developement.
 
 
+Load phonons from Phonopy and ASE
+---------------------------------
+
+Often, you may have to load a dynamical matrix from other sources than quantum-espresso.
+The two most common file formats are the Phonopy and the ASE calculation.
+
+For phonopy, we expect you generate a FORCE_CONSTANTS file and a phonopy.yaml file containing the information about the structure and the atoms in the supercell.
+
+NOTE: Up to version 1.0 the Phonopy importer assumes the FORCE_CONSTANTS and the structure are written in Rydberg atomic units. This will probably change in the near future.
+
+.. code::
+
+   import cellconstructor as CC
+   import cellconstructor.Phonons
+
+   # Load the dynamical matrix in phonopy format
+   dyn = CC.Phonons.Phonons()
+   dyn.load_phonopy("path/to/phonopy.yaml")
+
+   # Save as new_dyn in quantum espresso format
+   dyn.save_qe("new_dyn")
+
+   # Save in the phonopy format
+   dyn.save_phonopy("path/to/directory")
+
+Optionally, it is possible to provide also the path to the FORCE_CONSTANTS file, which by default is assumed to be in the same directory as the phonopy.yaml.
+This script can be employed to convert from Phonopy to quantum espresso file format.
+
+In the same way, it is possible to generate the FORCE_CONSTANTS file with the method save_phonopy. Here, you just need to specify the directory.
+Instead of the phonopy.yaml, the unitcell.in in quantum espresso format is generated. Phonopy is able to read this file.
+
+
+The ASE calculator can be used to directly compute the dynamical matrix from finite displacements.
+Once you have your ase.phonons.Phonons object, you can convert it into a CellConstructor Phonons object using the method get_dyn_from_ase_phonons.
+
+.. code::
+   
+   import ase
+   from ase.build import bulk
+   from ase.calculators.emt import EMT
+   from ase.phonons import Phonons
+   
+   import cellconstructor as CC, cellconstructor.Phonons
+
+   # Here the code to get the ase.phonon.Phonons object
+   # Setup crystal and EMT calculator
+   atoms = bulk('Al', 'fcc', a=4.05)
+
+   # Phonon calculator with ASE
+   N = 6
+   ph = Phonons(atoms, EMT(), supercell=(N, N, N), delta=0.05)
+   ph.run()
+
+   # Read forces and assemble the dynamical matrix
+   ph.read(acoustic=True)
+   ph.clean()
+
+   # Convert into the cellconstructor and save in quantum espresso format
+   dyn = CC.get_dyn_from_ase_phonons(ph)
+   dyn.save_qe("my_dyn_computed_with_ase")
+
+
+
 
 Generate a video of phonon vibrations
 -------------------------------------

cellconstructor/Phonons.py

@@ -1240,7 +1240,12 @@ def save_qe(self, filename, full_name = False):
             fp.write("*" * 75 + "\n")
             fp.close()
 
-    def save_phononpy(self, supercell_size = (1,1,1)):
+    def save_phononpy(self, *args, **kwargs):
+        "Mapping to save_phonopy"
+        warnings.warn("Deprecated, use save_phonopy instead.")
+        self.save_phonopy(*args, **kwargs)
+
+    def save_phonopy(self, path = ".", supercell_size = None):
         """
         EXPORT THE DYN IN THE PHONONPY FORMAT
         =====================================
@@ -1254,16 +1259,20 @@ def save_phononpy(self, supercell_size = (1,1,1)):
 
         Parameters
         ----------
+            path: str
+                Path to the directory in which the FORCE_CONSTANTS and unitcell.in files are created.
             supercell_size : list of 3
                 The supercell that defines the dynamical matrix, note phononpy 
-                works in the supercell.
+                works in the supercell. If none, it is inferred from the q points
 
 
         """
+        if supercell_size is None:
+            supercell_size = self.GetSupercell()
 
         # Save it into the phononpy in the supercell
         superdyn = self.GenerateSupercellDyn(supercell_size)
-        filename = "FORCE_CONSTANTS"
+        filename = os.path.join(path, "FORCE_CONSTANTS")
 
         nat_sc = superdyn.structure.N_atoms
         nat = self.structure.N_atoms
@@ -1314,7 +1323,7 @@ def save_phononpy(self, supercell_size = (1,1,1)):
             lines.append("%s  %16.8f   %16.8f   %16.8f\n" % (atm, cov_vect[0], cov_vect[1], cov_vect[2]))
 
 
-        f = open("unitcell.in", "w")
+        f = open(os.path.join(path, "unitcell.in"), "w")
         f.writelines(lines)
         f.close()